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Placing your application in sandbox_mode will ensure that only the people who are allowed to see the application have access to it.

You can also add your applications to your own un-published Facebook page, that way no one will be able to search for your page or application either.

A mixture of sandbox_mode and an un-published page should be the safe way to go. Check out the Application Security page in Facebook's documentation for exact explanations of sandbox_mode and the roles you can give users in your application.